Changes for page The FLASH HDF5 structure

Last modified by sndueste on 2025/02/06 10:55

From 5.1 to 4.1

From version 4.1

edited by sendels
on 2019/08/09 12:45

Change comment: added links

To version 1.1

edited by sendels
on 2019/05/15 12:57

Change comment: There is no comment for this version

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Title

@@ -1,1 +1,1 @@
--The FLASH HDF5 structure
++Information about the FLASH HDF5 structure

Content

@@ -2,22 +2,22 @@
  \\
--* [[General information about HDF5>>doc:||anchor="General information about HDF5"]]
--* [[FLASH HDF5 structure>>doc:||anchor="FLASH HDF5 structure"]]
--* [[Most popular FLASH parameters and their names in HDF5>>doc:||anchor="Most popular FLASH parameters and their names in HDF5"]]
--** [[FLASH1>>doc:||anchor="FLASH1"]]
--*** [[Beamline info (FLASH1)>>doc:||anchor="Beamline info (FLASH1)"]]
--*** [[Photon Diagnostics SASE / Spectrometer (FLASH1)>>doc:||anchor="Photon Diagnostics SASE / Spectrometer (FLASH1)"]]
--*** [[Electron Beam properties (FLASH1)>>doc:||anchor="Electron Beam properties (FLASH1)"]]
--*** [[Timing information, rep rate etc.(FLASH1)>>doc:||anchor="Timing information, rep rate etc.(FLASH1)"]]
--*** [[Pump Probe Laser (FLASH1)>>doc:||anchor="Pump Probe Laser (FLASH1)"]]
--*** [[User Data (FLASH1)>>doc:||anchor="User Data (FLASH1)"]]
--** [[FLASH2>>doc:||anchor="FLASH2"]]
--** [[HDF5 structure revisions>>doc:||anchor="HDF5 structure revisions"]]
--* [[Example code showing how to access HDF5 files>>doc:||anchor="Example code showing how to access HDF5 files"]]
--** [[Samples how to read HDF5 with Matlab>>doc:||anchor="Samples how to read HDF5 with Matlab"]]
--** [[How to read HDF5 with Python via FLASHH5>>doc:||anchor="How to read HDF5 with Python via FLASHH5"]]
--* [[HDF5 and DOOCS>>doc:||anchor="HDF5 and DOOCS"]]
++* General information about HDF5
++* FLASH HDF5 structure
++* Most popular FLASH parameters and their names in HDF5
++** FLASH1
++*** Beamline info (FLASH1)
++*** Photon Diagnostics: SASE / Spectrometer (FLASH1)
++*** Electron Beam properties (FLASH1)
++*** Timing information, rep rate etc.(FLASH1)
++*** Pump Probe Laser (FLASH1)
++*** User Data (FLASH1)
++** FLASH2
++** HDF5 structure revisions
++* Example code showing how to access HDF5 files
++** Samples how to read HDF5 with Matlab
++** How to read HDF5 with Python via FLASHH5
++* HDF5 and DOOCS
  \\
@@ -33,7 +33,7 @@
  {{code language="none"}}> module load xray{{/code}}
  {{code language="none"}}> hdfview{{/code}}
--[[Contents>>doc:||anchor="Contents"]]
++\\
  == FLASH HDF5 structure ==
@@ -44,12 +44,12 @@
  * Beamlines
  * Experiment
  * Timing
--[[~[~[image:url:http://hasfweb.desy.de/pub/Setup/HDF5main/HDF5_structure.jpg~|~|alt="HDF5_structure.jpg" width="700" height="500"~]~]>>attach:HDF5_structure.jpg]]
++[[image:url:http://hasfweb.desy.de/pub/Setup/HDF5main/HDF5_structure.jpg||alt="HDF5_structure.jpg" width="700" height="500"]]
  A detailled description of (most) channels can be found in the lower part of the hdf5 viewer:
--[[~[~[image:url:http://hasfweb.desy.de/pub/Setup/HDF5main/HDF5_structure_desc.jpg~|~|alt="HDF5_structure_desc.jpg" width="341" height="413"~]~]>>attach:HDF5_structure_desc.jpg]]
++[[image:url:http://hasfweb.desy.de/pub/Setup/HDF5main/HDF5_structure_desc.jpg||alt="HDF5_structure_desc.jpg" width="341" height="413"]]
--[[Contents>>doc:||anchor="Contents"]]
++\\
  \\
@@ -96,7 +96,7 @@
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}TTF2.FEL/BLFILTERS1/FILTER1/FW.MOTOR.POS{{/code}}
  DAQ channel: {{code language="none"}}TTF2.FEL/BLFILTERS1/FILTER1/FW.MOTOR.POS{{/code}}
--desc: Position of the BL filterwheel 1 - to correlate with the filter material please look [[here>>doc:FLASH.Filter history (BL filterwheel 12)]]
++desc: Position of the BL filterwheel 1 - to correlate with the filter material please look [[here>>url:http://hasfweb.desy.de/bin/view/Setup/FilterHistory||shape="rect" class="twikiLink"]]
  units: degree
  \\
@@ -104,7 +104,7 @@
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}TTF2.FEL/BLFILTERS2/FILTER2/FW.MOTOR.POS{{/code}}
  DAQ channel: {{code language="none"}}TTF2.FEL/BLFILTERS2/FILTER2/FW.MOTOR.POS{{/code}}
--desc: Position of the BL filterwheel 2 - to correlate with the filter material please look [[here>>doc:FLASH.Filter history (BL filterwheel 12)]]
++desc: Position of the BL filterwheel 2 - to correlate with the filter material please look [[here>>url:http://hasfweb.desy.de/bin/view/Setup/FilterHistory||shape="rect" class="twikiLink"]]
  units: degree
  \\
@@ -132,9 +132,9 @@
  units: degree
  \\
--[[Contents>>doc:||anchor="Contents"]]
++\\
--==== Photon Diagnostics SASE / Spectrometer (FLASH1) ====
++==== Photon Diagnostics: SASE / Spectrometer (FLASH1) ====
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy tunnel{{/code}}
  //always saved (PBD)//
@@ -148,7 +148,7 @@
  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT34/VAL{{/code}}
  DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENERGYPULSE.USER{{/code}}
  desc :Energy per pulse Tunnel (from e-) - the values are set to "0" if there was no SASE beam in the FEL
--units : a.u. (more or less µJ but need to be calibrated with the "Average energy" for good precision) [[see here for help>>doc:FLASH.Calibrating the pulse resolved (electron) data from GMD]]
++units : a.u. (more or less µJ but need to be calibrated with the "Average energy" for good precision) [[see here for help>>url:http://hasfweb.desy.de/bin/view/Setup/CalibrateGMDSignals||shape="rect" class="twikiLink"]]
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel (raw){{/code}}
  //always saved (PBD)//
@@ -155,7 +155,7 @@
  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT14/VAL{{/code}}
  DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENERGYPULSE.FF{{/code}}
  desc :Energy per pulse Tunnel (from e-) - uncorrected values. There are also values saved if there was no beam ... just background noise
--units : a.u. (more or less µJ but need to be calibrated with the "Average energy" for good precision) [[see here for help>>doc:FLASH.Calibrating the pulse resolved (electron) data from GMD]]
++units : a.u. (more or less µJ but need to be calibrated with the "Average energy" for good precision) [[see here for help>>url:http://hasfweb.desy.de/bin/view/Setup/CalibrateGMDSignals||shape="rect" class="twikiLink"]]
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy BDA{{/code}}
  //always saved (PBD)//
@@ -169,7 +169,7 @@
  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT35/VAL{{/code}}
  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENERGYPULSE.USER{{/code}}
  desc :Energy per pulse BDA (from e-) - the values are set to "0" if there was no SASE beam in the FEL
--units : a.u. (more or less µJ but need to be calibrated with the "Average energy" for good precision) [[see here for help>>doc:FLASH.Calibrating the pulse resolved (electron) data from GMD]]
++units : a.u. (more or less µJ but need to be calibrated with the "Average energy" for good precision) [[see here for help>>url:http://hasfweb.desy.de/bin/view/Setup/CalibrateGMDSignals||shape="rect" class="twikiLink"]]
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy BDA (raw){{/code}}
  //always saved (PBD)//
@@ -176,13 +176,13 @@
  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT15/VAL{{/code}}
  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENERGYPULSE.FF{{/code}}
  desc :Energy per pulse BDA (from e-) - uncorrected values. There are also values saved if there was no beam ... just background noise
--units : a.u. (more or less µJ but need to be calibrated with the "Average energy" for good precision) [[see here for help>>doc:FLASH.Calibrating the pulse resolved (electron) data from GMD]]
++units : a.u. (more or less µJ but need to be calibrated with the "Average energy" for good precision) [[see here for help>>url:http://hasfweb.desy.de/bin/view/Setup/CalibrateGMDSignals||shape="rect" class="twikiLink"]]
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position BDA horizontal{{/code}}
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IX.POS{{/code}}
  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IX.POS{{/code}}
--desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASH.Gas Monitor Detector]] (BDA, x=horizontal)
++desc :Beam position of the photon Beam determined by the [[GMD>>url:http://hasfweb.desy.de/bin/view/Setup/GMD||shape="rect" class="twikiLink"]] (BDA, x=horizontal)
  units : mm
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position BDA vertical{{/code}}
@@ -189,7 +189,7 @@
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IY.POS{{/code}}
  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IY.POS{{/code}}
--desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASH.Gas Monitor Detector]] (BDA, y=vertical)
++desc :Beam position of the photon Beam determined by the [[GMD>>url:http://hasfweb.desy.de/bin/view/Setup/GMD||shape="rect" class="twikiLink"]] (BDA, y=vertical)
  units : mm
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position tunnel horizontal{{/code}}
@@ -196,7 +196,7 @@
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.TUNNEL/IX.POS{{/code}}
  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.TUNNEL/IX.POS{{/code}}
--desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASH.Gas Monitor Detector]] (TUNNEL, x=horizontal)
++desc :Beam position of the photon Beam determined by the [[GMD>>url:http://hasfweb.desy.de/bin/view/Setup/GMD||shape="rect" class="twikiLink"]] (TUNNEL, x=horizontal)
  units : mm
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position tunnel vertical{{/code}}
@@ -203,7 +203,7 @@
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.TUNNEL/IY.POS{{/code}}
  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.TUNNEL/IY.POS{{/code}}
--desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASH.Gas Monitor Detector]] (TUNNEL, y=vertical)
++desc :Beam position of the photon Beam determined by the [[GMD>>url:http://hasfweb.desy.de/bin/view/Setup/GMD||shape="rect" class="twikiLink"]] (TUNNEL, y=vertical)
  units : mm
  {{code language="none"}}/FL1/Photon Diagnostic/Wavelength/Tunnelspectrometer/wavelength{{/code}}
@@ -269,7 +269,7 @@
  desc : increment value (in nm) for each pixel for the wavelength axis of the XUV Spectrum measured with the "PG spectrometer"
  units : nm
--[[Contents>>doc:||anchor="Contents"]]
++\\
  ==== Electron Beam properties (FLASH1) ====
@@ -334,7 +334,7 @@
  DOOCS prop : {{code language="none"}}TTF2.DAQ/ENERGY.DOGLEG/E_INTRA_MEAN/VAL{{/code}}
  DAQ channel: {{code language="none"}}PBD.ENERGY.DOGLEG/E_MEAN{{/code}}
  desc: electron bunch energy (average over the bunch train)
--units: (% class="twikiNewLink" %)MeV(%%)
++units: (% class="twikiNewLink" %)[[MeV>>url:http://hasfweb.desy.de/bin/edit/Setup/MeV?topicparent=Setup.HDF5main;nowysiwyg=0||rel="nofollow" shape="rect"]](%%)
  \\
  {{code language="none"}}/FL1/Electron Diagnostic/Electron energy/pulse resolved energy{{/code}}
@@ -342,7 +342,7 @@
  DOOCS prop : {{code language="none"}}TTF2.DAQ/ENERGY.DOGLEG/E_SPECT/VAL.TD{{/code}}
  DAQ channel: {{code language="none"}}PBD.ENERGY.DOGLEG/E_SPECT{{/code}}
  desc: electron bunch energy bunch resolved
--units: (% class="twikiNewLink" %)MeV(%%)
++units: (% class="twikiNewLink" %)[[MeV>>url:http://hasfweb.desy.de/bin/edit/Setup/MeV?topicparent=Setup.HDF5main;nowysiwyg=0||rel="nofollow" shape="rect"]](%%)
  \\
  \\
@@ -355,7 +355,7 @@
  units: nm
  \\
--[[Contents>>doc:||anchor="Contents"]]
++\\
  \\
@@ -436,7 +436,7 @@
  third column: Train ID of FLASH
  \\
--[[Contents>>doc:||anchor="Contents"]]
++\\
  \\
@@ -466,7 +466,7 @@
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}FLASH.SYNC/F1PPL.LASER_LOCK/28C.F1PPL1.CONTROLLER/ADV_CTRL_MANAGER.0.PID_INPUT_JITTER.2.RD{{/code}}
  DAQ channel: {{code language="none"}}FLASH.SYNC/F1PPL.LASER_LOCK/28C.F1PPL1.CONTROLLER/ADV_CTRL_MANAGER.0.PID_INPUT_JITTER.2.RD{{/code}}
--desc: rms jitter of the GECCO (% class="twikiNewLink" %)TiSa(%%) Oscillator units: fs
++desc: rms jitter of the GECCO (% class="twikiNewLink" %)[[TiSa>>url:http://hasfweb.desy.de/bin/edit/Setup/TiSa?topicparent=Setup.HDF5main;nowysiwyg=0||rel="nofollow" shape="rect"]](%%) Oscillator units: fs
  \\
@@ -478,7 +478,7 @@
  \\
--[[Contents>>doc:||anchor="Contents"]]
++\\
  \\
@@ -488,7 +488,7 @@
  ===== GHz ADCs =====
--ADC traces of the (SPDevices 412) GHZ ADCs available for the users . More information about the ADCs can be found [[here>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).MTCA ADCs.WebHome]]
++ADC traces of the (SPDevices 412) GHZ ADCs available for the users . More information about the ADCs can be found [[here>>url:http://hasfweb.desy.de/bin/view/Setup/MtcaAdc||shape="rect" class="twikiLink"]]
  //saved on DEMAND in the user DAQ//
  \\The HDF5 names for the ADC traces are depending on the beamline :
  \\PG Beamline:
@@ -528,17 +528,16 @@
  \\
--[[Contents>>doc:||anchor="Contents"]]
++\\
  === FLASH2 ===
  \\
--(% class="wrapped" %)
  |=(((
--DAQ name
++[[DAQ name>>url:http://hasfweb.desy.de/bin/view/Setup/HDF5main?sortcol=0;table=1;up=0#sorted_table||title="Sort by this column" rel="nofollow" shape="rect"]]
  )))|=(((
--HDF5 name
++[[HDF5 name>>url:http://hasfweb.desy.de/bin/view/Setup/HDF5main?sortcol=1;table=1;up=0#sorted_table||title="Sort by this column" rel="nofollow" shape="rect"]]
  )))
  |(((
  FLASH.UTIL/FL2.UND.MOTOR/FL2SASE3/GAP
@@ -723,7 +723,7 @@
  \\
--[[Contents>>doc:||anchor="Contents"]]
++\\
  === HDF5 structure revisions ===
@@ -737,11 +737,10 @@
  \\
--(% class="wrapped" %)
  |=(((
--earlier HDF path (vers. 0.2)
++[[earlier HDF path (vers. 0.2)>>url:http://hasfweb.desy.de/bin/view/Setup/HDF5main?sortcol=0;table=2;up=0#sorted_table||title="Sort by this column" rel="nofollow" shape="rect"]]
  )))|=(((
--is now (vers. 0.3)
++[[is now (vers. 0.3)>>url:http://hasfweb.desy.de/bin/view/Setup/HDF5main?sortcol=1;table=2;up=0#sorted_table||title="Sort by this column" rel="nofollow" shape="rect"]]
  )))
  |(((
  /Photon Diagnostic/GMD/Beam position/position BDA x
@@ -836,7 +836,7 @@
  \\
--[[Contents>>doc:||anchor="Contents"]]
++\\
  \\
@@ -895,16 +895,14 @@
  GMD_Spectrum=h5read(hdf5file,'/Photon Diagnostic/GMD/Pulse resolved energy/energy BDA',[1 Start_event],[40 Number_of_events] );
  )))
--[[Contents>>doc:||anchor="Contents"]]
++\\
  === How to read HDF5 with Python via FLASHH5 ===
--With [[FlashH5>>doc:FLASHUSER.FLASHH5 for easier access of FLASH's HDF5 files]] we provide h5py based examples to access and evaluate FLASH's HDF5 files.
++With [[FlashH5>>url:http://hasfweb.desy.de/bin/view/Setup/FlashH5||shape="rect" class="twikiLink"]] we provide h5py based examples to access and evaluate FLASH's HDF5 files.
  \\
  == HDF5 and DOOCS ==
--Here is an outdated [[list with the available properties that are always saved (PBD) for FLASH1 as>>attach:FLASH1__DaqChannel2HdfNamePbd.xlsx]] HDF5 names and the corresponding DOOCS names
--
--[[Contents>>doc:||anchor="Contents"]]
++Here is an outdated [[list with the available properties that are always saved (PBD) for FLASH1 as>>url:http://hasfweb.desy.de/pub/Setup/HDF5main/FLASH1__DaqChannel2HdfNamePbd.xlsx||shape="rect"]] HDF5 names and the corresponding DOOCS names

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